Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002315.1 Hibiscus syriacus cultivar Beakdansim tig00004715_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 78005
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3199 original size:14 final size:14
Alignment explanation
Indices: 3180--3213 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3170 CATCAATTAA
3180 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3194 ACAAATCATCTTTT
1 ACAAATCAACATTT
3208 ACAAAT
1 ACAAAT
3214 TAATTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:5096 original size:20 final size:20
Alignment explanation
Indices: 5073--5126 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
5063 GAAACTTAAA
5073 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
5093 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
5113 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
5127 TGAAAATGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:5217 original size:19 final size:19
Alignment explanation
Indices: 5195--5291 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
5185 GAAACACAAA
5195 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
5214 TCGCGTTGCG-TTTT--TG
1 TCGCATTGCGATTTTCATT
*
5230 TCG--TTGCGTTTTTCATT
1 TCGCATTGCGATTTTCATT
* *
5247 TCGCATTGCG-GTTT--TG
1 TCGCATTGCGATTTTCATT
5263 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
5280 TCGCATTGCGAT
1 TCGCATTGCGAT
5292 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 10 0.16
15 7 0.11
16 8 0.13
17 8 0.13
18 7 0.11
19 21 0.34
ACGTcount: A:0.09, C:0.20, G:0.23, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5243 original size:33 final size:33
Alignment explanation
Indices: 5200--5289 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
5190 ACAAATCGCA
* *
5200 TTGCGATTTTCATTTCGCGTTGCGTTTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGGTTTTGTCG
*
5233 TTGCGTTTTTCATTTCGCATTGCGGTTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGGTTTTGTCG
5266 TTGCGATTTTCATTTCGCATTGCG
1 TTGCGATTTTCATTTCGCATTGCG
5290 ATAGCCATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.08, C:0.19, G:0.23, T:0.50
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGGTTTTGTCG
Found at i:5310 original size:20 final size:19
Alignment explanation
Indices: 5276--5330 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
5266 TTGCGATTTT
*
5276 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
5295 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
5315 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
5331 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:5888 original size:18 final size:18
Alignment explanation
Indices: 5865--5913 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
5855 CGGGTCAATC
5865 AGGTGATGGCTCCGGGTG
1 AGGTGATGGCTCCGGGTG
* *
5883 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCCGGGTG
5901 AGGTGATGGCTCC
1 AGGTGATGGCTCC
5914 CGAAGTGGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.14, C:0.16, G:0.45, T:0.24
Consensus pattern (18 bp):
AGGTGATGGCTCCGGGTG
Found at i:7265 original size:20 final size:20
Alignment explanation
Indices: 7232--7289 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
7222 AATAGTTTCT
** *
7232 GAAAATGAAAATCGCAATAC
1 GAAAATGACTATCGCAACAC
*
7252 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACAC
**
7272 GAATTTGACTATCGCAAC
1 GAAAATGACTATCGCAAC
7290 GAGAGAATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (20 bp):
GAAAATGACTATCGCAACAC
Found at i:7822 original size:20 final size:20
Alignment explanation
Indices: 7796--7868 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
7786 GATTATGTAT
7796 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
7816 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
**
7836 TATCTTGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
7856 TATCTCGTTGCGA
1 TATCGCGTTGCGA
7869 TTTTGTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:7905 original size:20 final size:20
Alignment explanation
Indices: 7796--7902 Score: 99
Period size: 20 Copynumber: 5.3 Consensus size: 20
7786 GATTATGTAT
*
7796 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
7816 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
** *
7836 TATCTTGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
7856 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
*
7877 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
7897 TATCGC
1 TATCGC
7903 ATTACGATTT
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 3 0.04
20 55 0.76
21 12 0.17
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:8606 original size:20 final size:20
Alignment explanation
Indices: 8567--8623 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
8557 TTTCATTTTA
*
8567 CATTCACATCTTTGCATTTG
1 CATTCACATCTTTACATTTG
* *
8587 CATTCGCATCTTTACGTTTG
1 CATTCACATCTTTACATTTG
* *
8607 TATTTACAT-TTT-CATTT
1 CATTCACATCTTTACATTT
8624 TTTACATTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
18 4 0.13
19 3 0.10
20 23 0.77
ACGTcount: A:0.19, C:0.21, G:0.09, T:0.51
Consensus pattern (20 bp):
CATTCACATCTTTACATTTG
Found at i:8951 original size:42 final size:42
Alignment explanation
Indices: 8890--8973 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
8880 AGAGATGATT
* * * *
8890 GATCAAGTAAAAAAGTTCCAGGGTGATTCAAATGAACAAATG
1 GATCAAGGAAAAAAGTTCCAAGATGATTCAAAAGAACAAATG
*
8932 GATCAAGCGAAAAAA-TTCCAAGATGATTCAAAAGAGCAAATG
1 GATCAAG-GAAAAAAGTTCCAAGATGATTCAAAAGAACAAATG
8974 ACAAAACTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 30 0.83
43 6 0.17
ACGTcount: A:0.48, C:0.13, G:0.20, T:0.19
Consensus pattern (42 bp):
GATCAAGGAAAAAAGTTCCAAGATGATTCAAAAGAACAAATG
Found at i:13254 original size:33 final size:31
Alignment explanation
Indices: 13217--13292 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
13207 GAAGGGCATT
*
13217 TTGAAGGTCCATATTATCAATGATTGGGACATC
1 TTGAAGGTCCATATCATC-ATG-TTGGGACATC
* * *
13250 TTGAAGATTCATATCATCATGTTGGGACATT
1 TTGAAGGTCCATATCATCATGTTGGGACATC
13281 TTGAAGGTCCAT
1 TTGAAGGTCCAT
13293 TTTGACCATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 19 0.51
32 3 0.08
33 15 0.41
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (31 bp):
TTGAAGGTCCATATCATCATGTTGGGACATC
Found at i:15253 original size:137 final size:137
Alignment explanation
Indices: 15080--15595 Score: 684
Period size: 137 Copynumber: 3.8 Consensus size: 137
15070 GTGTTCATCA
* * * *
15080 ACATCAACCTTAGATAGCCAGACGTCCTCATAACGAAGGAACTGTGTTATCTCAAATATCTTTAA
1 ACATCATCCTTAGACAACCAGACGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCTTTAA
*
15145 AGATGGACAGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCTTCATCAAGA
66 AGATGGACAGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCAAGA
15210 ATGAGTC
131 ATGAGTC
* *
15217 ACATCATCCTTAGACAACCAGATGTCCTCATCACGAAGGAACTGTGTTATC-CTAAATGTC-TTA
1 ACATCATCCTTAGACAACCAGACGTCCTCATCACGAAGGAACTGTGTTATCTC-AAATATCTTTA
* *
15280 AAGATGG-CAAAATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCAT
65 AAGATGGAC-AGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCAA
*
15344 GAAGGAGTC
129 GAATGAGTC
* *
15353 ACATCATCCTTAGACAGCCAGACGTCCTCATCACGAATGAACTGTGTTATCTCAAATAT-TTTCA
1 ACATCATCCTTAGACAACCAGACGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCTTT-A
** * * *
15417 AAGAT-GATCAGAACTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
65 AAGATGGA-CAGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCAA
15481 GAATGAG-C
129 GAATGAGTC
* * * * * * * *
15489 AACATCATTCTTAGATAACCAGATGTGCTCATCATGAAAGAACAGTGTTATCTCAAATATCTTCA
1 -ACATCATCCTTAGACAACCAGACGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCTTTA
* * * *
15554 AAGATGGCCAGATGTCCTCATCATGAAAGAACAATGTTATCT
65 AAGATGGACAGATGTCCTCATCACGAAGGAACAATGTCATCT
15596 CAAATATCTT
Statistics
Matches: 332, Mismatches: 37, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
135 1 0.00
136 128 0.39
137 199 0.60
138 4 0.01
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (137 bp):
ACATCATCCTTAGACAACCAGACGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCTTTAA
AGATGGACAGATGTCCTCATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCAAGA
ATGAGTC
Found at i:15592 original size:54 final size:54
Alignment explanation
Indices: 15507--15644 Score: 222
Period size: 54 Copynumber: 2.6 Consensus size: 54
15497 TCTTAGATAA
* *
15507 CCAGATGTGCTCATCATGAAAGAACAGTGTTATCTCAAATATCTTCAAAGATGG
1 CCAGATGTCCTCATCATGAAAGAACAATGTTATCTCAAATATCTTCAAAGATGG
*
15561 CCAGATGTCCTCATCATGAAAGAACAATGTTATCTCAAATATCTTTAAAGATGG
1 CCAGATGTCCTCATCATGAAAGAACAATGTTATCTCAAATATCTTCAAAGATGG
* * *
15615 CCAGACGTCCTCATCACGAAGGAACAATGT
1 CCAGATGTCCTCATCATGAAAGAACAATGT
15645 CATCCACCGA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 78 1.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (54 bp):
CCAGATGTCCTCATCATGAAAGAACAATGTTATCTCAAATATCTTCAAAGATGG
Found at i:15628 original size:191 final size:191
Alignment explanation
Indices: 15369--15781 Score: 616
Period size: 191 Copynumber: 2.2 Consensus size: 191
15359 TCCTTAGACA
* ** *
15369 GCCAGACGTCCTCATCACGAATGAACTGTGTTATCTCAAATATTTTCAAAGATGATCAGAACTCC
1 GCCAGACGTCCTCATCACGAAAGAACAATGTTATCTCAAATATTTTCAAAGATGACCAGAACTCC
*
15434 TCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAATGAGCAACATCATTC
66 TCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCAACATCATTC
* *
15499 TTAGATAACCAGATGTGCTCATCATGAAAGAA-CAGTGTTATCTCAAATATCTTCAAAGATG
131 TTAGATAACCAGATGTCCTCATCACGAAAGAACCA-TGTTATCTCAAATATCTTCAAAGATG
* * *
15560 GCCAGATGTCCTCATCATGAAAGAACAATGTTATCTCAAATATCTTT-AAAGATGGCCAG-ACGT
1 GCCAGACGTCCTCATCACGAAAGAACAATGTTATCTCAAATAT-TTTCAAAGATGACCAGAAC-T
*
15623 CCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCAACATTAT
64 CCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCAACATCAT
* * * *
15688 TCTTATATAGCCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTTAAAGATG
129 TCTTAGATAACCAGATGTCCTCATCACGAAAGAACCATGTTATCTCAAATATCTTCAAAGATG
* * *
15751 GCTAAACGTCCTCATCACGAAGGAACAATGT
1 GCCAGACGTCCTCATCACGAAAGAACAATGT
15782 CATCCACTGA
Statistics
Matches: 199, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
190 2 0.01
191 192 0.96
192 5 0.03
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (191 bp):
GCCAGACGTCCTCATCACGAAAGAACAATGTTATCTCAAATATTTTCAAAGATGACCAGAACTCC
TCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCAACATCATTC
TTAGATAACCAGATGTCCTCATCACGAAAGAACCATGTTATCTCAAATATCTTCAAAGATG
Found at i:15678 original size:328 final size:327
Alignment explanation
Indices: 15234--15918 Score: 927
Period size: 328 Copynumber: 2.1 Consensus size: 327
15224 CCTTAGACAA
* ** * *
15234 CCAGATGTCCTCATCACGAAGGAACTGTGTTATCCTAAATGTCTTAAAGATGGCAAAATGTCCTC
1 CCAGATGTCCTCATCATGAAGGAACAATGTTATCCTAAATATCTTAAAGATGGCAAAACGTCCTC
* *
15299 ATCACGAAGGAACAATGTCATCTACCAATCAGAACTCCTCATCATGAAGGAGTC-ACATCATCCT
66 ATCACGAAGGAACAATGTCATCCACCAATCAGAACTCCTCATCACGAAGGAG-CAACATCATCCT
* ** *
15363 TAGACAGCCAGACGTCCTCATCACGAATGAACTGTGTTATCTCAAATAT-TTTCAAAGAT-GATC
130 TAGACAGCCAGACGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTT-AAAGATGGCT-
* *
15426 AGAAC-TCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAATGAGCA
193 A-AACGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGAAGGAGC-
* * * * *
15490 AC-A-TCATTCTTAGATAACCAGATGTGCTCATCATGAAA-GAACAGTGTTATCTCAAATATCTT
256 -CGAGTCATCCTCAGATAACCAGACGTCCTCATCA-CAAAGGAACAGTGTTATCTCAAATATCTT
15552 CAAAGATGG
319 CAAAGATGG
* * *
15561 CCAGATGTCCTCATCATGAAAGAACAATGTTAT-CTCAAATATCTTTAAAGATGGCCAGACGTCC
1 CCAGATGTCCTCATCATGAAGGAACAATGTTATCCT-AAATATC-TTAAAGATGGCAAAACGTCC
* * *
15625 TCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCAACATTATTC
64 TCATCACGAAGGAACAATGTCATCCACCAATCAGAACTCCTCATCACGAAGGAGCAACATCATCC
* * *
15690 TTATATAGCCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTTAAAGATGGCTA
129 TTAGACAGCCAGACGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTTAAAGATGGCTA
* *
15755 AACGTCCTCATCACGAAGGAACAATGTCATCCACTGACCAGAACTCCTCATCACGTAGGAGCCGA
194 AACGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGAAGGAGCCGA
*
15820 GTCATCCTCAGATAACCAGACGTCCTCATCACAAAGGAACCGTGTTATCTCAAATATCTTCAAAG
259 GTCATCCTCAGATAACCAGACGTCCTCATCACAAAGGAACAGTGTTATCTCAAATATCTTCAAAG
15885 ATGG
324 ATGG
* * * *
15889 CTAAACGTTCTCATCATGAAGGAACAATGT
1 CCAGATGTCCTCATCATGAAGGAACAATGT
15919 CATACACCAG
Statistics
Matches: 314, Mismatches: 35, Indels: 17
0.86 0.10 0.05
Matches are distributed among these distances:
326 3 0.01
327 43 0.14
328 263 0.84
329 5 0.02
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (327 bp):
CCAGATGTCCTCATCATGAAGGAACAATGTTATCCTAAATATCTTAAAGATGGCAAAACGTCCTC
ATCACGAAGGAACAATGTCATCCACCAATCAGAACTCCTCATCACGAAGGAGCAACATCATCCTT
AGACAGCCAGACGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTTAAAGATGGCTAAA
CGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGAAGGAGCCGAGT
CATCCTCAGATAACCAGACGTCCTCATCACAAAGGAACAGTGTTATCTCAAATATCTTCAAAGAT
GG
Found at i:15806 original size:137 final size:137
Alignment explanation
Indices: 15555--15926 Score: 523
Period size: 137 Copynumber: 2.7 Consensus size: 137
15545 ATATCTTCAA
* * * * * *
15555 AGATGGCCAGATGTCCTCATCATGAAAGAACAATGTTATCTCAAATATCTTTAAAGATGGCCAGA
1 AGATAGCCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTTAAAGATGGCTAAA
*
15620 CGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCAAC-A
66 CGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGAAGGAGC--CGA
* * *
15684 -TTATTCTT
129 GTCATCCTC
*
15692 ATATAGCCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTTAAAGATGGCTAAA
1 AGATAGCCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTTAAAGATGGCTAAA
* *
15757 CGTCCTCATCACGAAGGAACAATGTCATCCACTGACCAGAACTCCTCATCACGTAGGAGCCGAGT
66 CGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGAAGGAGCCGAGT
15822 CATCCTC
131 CATCCTC
* * * * *
15829 AGATAACCAGACGTCCTCATCACAAAGGAACCGTGTTATCTCAAATATCTTCAAAGATGGCTAAA
1 AGATAGCCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTTAAAGATGGCTAAA
* * *
15894 CGTTCTCATCATGAAGGAACAATGTCATACACC
66 CGTCCTCATCACGAAGGAACAATGTCATCCACC
15927 AGTTGAATAT
Statistics
Matches: 210, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
135 1 0.00
136 1 0.00
137 208 0.99
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (137 bp):
AGATAGCCAGATGTCCTCATCACGAAGGAACCATGTTATCTCAAATATCTTTAAAGATGGCTAAA
CGTCCTCATCACGAAGGAACAATGTCATCCACCGACCAGAACTCCTCATCACGAAGGAGCCGAGT
CATCCTC
Found at i:17233 original size:118 final size:119
Alignment explanation
Indices: 17111--17324 Score: 258
Period size: 118 Copynumber: 1.8 Consensus size: 119
17101 ATATTTTATA
* *
17111 ATATTTTGAATTAAGACCATTAATTTAT-ATATTTTTACAA-TTTAATCAC-TGAGGTTTAATAT
1 ATATTTAGAATTAAGACCATTAATTT-TGATA-TTTTACAATTTTAATC-CTTGAGGTTTAAAAT
**
17173 TTTAATTTTAAATAATA-TTTTAGGAA-TATTTACACTAATAATACCTAGATTTCATG
63 AATAATTTTAAATAATATTTTTA-GAATTATTTACACTAATAATACCTAGATTTCATG
* *** * *
17229 ATATTTAGAATTAGGATTTTTAATTTTGATATTTTACAATTTTAATCCTTTAGTTTTAAAATAAT
1 ATATTTAGAATTAAGACCATTAATTTTGATATTTTACAATTTTAATCCTTGAGGTTTAAAATAAT
*
17294 AATTTTAAATATTATTTTTAGAATTATTTAC
66 AATTTTAAATAATATTTTTAGAATTATTTAC
17325 TATTATAGTA
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
117 10 0.12
118 58 0.73
119 12 0.15
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (119 bp):
ATATTTAGAATTAAGACCATTAATTTTGATATTTTACAATTTTAATCCTTGAGGTTTAAAATAAT
AATTTTAAATAATATTTTTAGAATTATTTACACTAATAATACCTAGATTTCATG
Found at i:24832 original size:60 final size:61
Alignment explanation
Indices: 24742--24879 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 61
24732 TAAATGTTTC
* *
24742 AATTTCATCCCTAAACTATGACTATAATTCTAAATTAGTCCTCAAAATTTT-GAACATTTT
1 AATTTCATCCCTAAACTACGACTATAATTCTAAATTAGTCCCCAAAATTTTCGAACATTTT
* * * **
24802 AATTTCATTCCTAAACTACGATCT-TCATTCTAAATTAGTCCCCAAACTTTTCGAACATTCC
1 AATTTCATCCCTAAACTACGA-CTATAATTCTAAATTAGTCCCCAAAATTTTCGAACATTTT
*
24863 AAATTCATCCC-AAACTA
1 AATTTCATCCCTAAACTA
24880 TACGTATATA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
60 49 0.73
61 18 0.27
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (61 bp):
AATTTCATCCCTAAACTACGACTATAATTCTAAATTAGTCCCCAAAATTTTCGAACATTTT
Found at i:25031 original size:29 final size:29
Alignment explanation
Indices: 24999--25086 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
24989 AGATGAATTT
24999 GGGATGGAATTAGAATATTCAAAAGTTTG
1 GGGATGGAATTAGAATATTCAAAAGTTTG
* * **
25028 GGGAT-CAATTTAGAATTAAGATC-ATGGTTTG
1 GGGATGGAA-TTAGAA-T-A-TTCAAAAGTTTG
*
25059 GGGATGGAATTAAAATATTCAAAAGTTT
1 GGGATGGAATTAGAATATTCAAAAGTTT
25087 AAGGATAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
28 4 0.09
29 17 0.39
30 2 0.05
31 17 0.39
32 4 0.09
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (29 bp):
GGGATGGAATTAGAATATTCAAAAGTTTG
Found at i:25118 original size:60 final size:58
Alignment explanation
Indices: 24996--25150 Score: 177
Period size: 60 Copynumber: 2.6 Consensus size: 58
24986 TTTAGATGAA
** * *
24996 TTTGGGATGGAATTAGAATATTCAAAAGTTTGGGGATCAATTTAGAATTAAGATCATGG
1 TTTGGGATGGAATTAGAATATTCAAAAGTTTAAGGATAAATTTAGAA-TAAGATCATAG
* *
25055 TTTGGGGATGGAATTAAAATATTCAAAAGTTTAAGGATAAATTTAGAA-AGAGAATTATAG
1 TTT-GGGATGGAATTAGAATATTCAAAAGTTTAAGGATAAATTTAGAATA-AG-ATCATAG
* ** *
25115 TTTGAGATCAAATTAGTATATTCAAAAGTTTAAGGA
1 TTTGGGATGGAATTAGAATATTCAAAAGTTTAAGGA
25151 CCAATTTAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
58 1 0.01
59 33 0.40
60 48 0.59
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.34
Consensus pattern (58 bp):
TTTGGGATGGAATTAGAATATTCAAAAGTTTAAGGATAAATTTAGAATAAGATCATAG
Found at i:34484 original size:3 final size:3
Alignment explanation
Indices: 34476--34530 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
34466 TCTAATTTTA
*
34476 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATGT -TT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT -ATT ATT ATT
34522 ATT ATT ATT
1 ATT ATT ATT
34531 TTTGCAGGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 1 0.02
3 42 0.89
4 4 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:36330 original size:19 final size:19
Alignment explanation
Indices: 36289--36331 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
36279 ATTCCTTTTG
* **
36289 TATGTACTTATTTTTATGT
1 TATGTACTTATTTATATCA
*
36308 TATGTATTTATTTATATCA
1 TATGTACTTATTTATATCA
36327 TATGT
1 TATGT
36332 GAATTAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (19 bp):
TATGTACTTATTTATATCA
Found at i:41118 original size:30 final size:31
Alignment explanation
Indices: 41082--41142 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
41072 GACGCAGAGT
**
41082 GCAAAGATCAAACCAAAG-AAAAAACAAAGA
1 GCAAAGAGAAAACCAAAGCAAAAAACAAAGA
* *
41112 GCAAAGAGAAAATCAAAGCAAAAATCAAAGA
1 GCAAAGAGAAAACCAAAGCAAAAAACAAAGA
41143 AAAAGCAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.66, C:0.15, G:0.15, T:0.05
Consensus pattern (31 bp):
GCAAAGAGAAAACCAAAGCAAAAAACAAAGA
Found at i:41135 original size:12 final size:11
Alignment explanation
Indices: 41113--41154 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
41103 AAACAAAGAG
41113 CAAAGAGAAAAT
1 CAAAGA-AAAAT
41125 CAAAGCAAAAAT
1 CAAAG-AAAAAT
*
41137 CAAAGAAAAAG
1 CAAAGAAAAAT
41148 CAAAGAA
1 CAAAGAA
41155 CAAAAGAGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 12 0.43
12 15 0.54
13 1 0.04
ACGTcount: A:0.69, C:0.12, G:0.14, T:0.05
Consensus pattern (11 bp):
CAAAGAAAAAT
Found at i:42347 original size:4 final size:4
Alignment explanation
Indices: 42330--42391 Score: 85
Period size: 4 Copynumber: 16.0 Consensus size: 4
42320 CTCGAGAAAA
*
42330 ACAT ACAT -CAAT ACAT ACAT ACAT ATAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT AC-AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
42378 AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT
42392 GATACATAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 2 0.04
3 1 0.02
4 48 0.92
5 1 0.02
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:42801 original size:36 final size:36
Alignment explanation
Indices: 42738--42846 Score: 119
Period size: 38 Copynumber: 2.9 Consensus size: 36
42728 AAAAAAACAA
* * * * *
42738 AAAAACAAAGTGTCGTCTCACTAGAGACAGTTTTCTT
1 AAAAACAAA-TTTTGTCTCGCTTGAGACACTTTTCTT
42775 AAAAACAAATTTTGTCTCGCTTGAGACAACTTTCTCTT
1 AAAAACAAATTTTGTCTCGCTTGAGAC-ACTTT-TCTT
* * *
42813 TAAAACAAATTATGTCTCGCTTGAGACATTTTTC
1 AAAAACAAATTTTGTCTCGCTTGAGACACTTTTC
42847 CACAAATTTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
36 16 0.26
37 17 0.27
38 29 0.47
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (36 bp):
AAAAACAAATTTTGTCTCGCTTGAGACACTTTTCTT
Found at i:42829 original size:38 final size:38
Alignment explanation
Indices: 42771--42906 Score: 123
Period size: 38 Copynumber: 3.8 Consensus size: 38
42761 GAGACAGTTT
* *
42771 TCTTAAAAACAAATTTTGTCTCGCTTGAGACAACTTTC
1 TCTTTAAAACAAATTATGTCTCGCTTGAGACAACTTTC
42809 TCTTTAAAACAAATTATGTCTCGCTTGAGAC-A---T-
1 TCTTTAAAACAAATTATGTCTCGCTTGAGACAACTTTC
** ** *
42842 T-TTT-CCACAAATT-T-T-GAGAATT-AGACAACTTTC
1 TCTTTAAAACAAATTATGTCTCG-CTTGAGACAACTTTC
42875 TCTTTAAAACAAATTATGTCTCGCTTGAGACA
1 TCTTTAAAACAAATTATGTCTCGCTTGAGACA
42907 TTTTTCCACA
Statistics
Matches: 74, Mismatches: 12, Indels: 24
0.67 0.11 0.22
Matches are distributed among these distances:
28 5 0.07
29 4 0.05
30 1 0.01
31 7 0.09
32 4 0.05
33 2 0.03
34 4 0.05
35 7 0.09
36 1 0.01
37 4 0.05
38 35 0.47
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (38 bp):
TCTTTAAAACAAATTATGTCTCGCTTGAGACAACTTTC
Found at i:42888 original size:66 final size:66
Alignment explanation
Indices: 42798--42929 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
42788 GTCTCGCTTG
*
42798 AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACATTTTTCCACAAATTTTGAGAAT
1 AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACATTTTTCCACAAATTTTGAAAAT
42863 T
66 T
42864 AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACATTTTTCCACAAATTTTGAAAAT
1 AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACATTTTTCCACAAATTTTGAAAAT
42929 T
66 T
42930 TTAAAACAAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (66 bp):
AGACAACTTTCTCTTTAAAACAAATTATGTCTCGCTTGAGACATTTTTCCACAAATTTTGAAAAT
T
Found at i:43119 original size:105 final size:102
Alignment explanation
Indices: 42932--43170 Score: 288
Period size: 105 Copynumber: 2.3 Consensus size: 102
42922 TGAAAATTTT
* * *
42932 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
*
42997 AAAAACAAAATTAATCTCACCTT-AGATTCTTGTTTCTTTC-
66 AAAAACAAAATTAATCTCA-CTTGAGA-TCAT-TTTC--TCA
* * *
43037 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
* * *
43101 ATTAAACAAAGTTGATCTCACTTGAGATCATTTTCTCA
66 A-AAAACAAAATTAATCTCACTTGAGATCATTTTCTCA
*
43139 AAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
43171 TCTAAAAACA
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
101 2 0.02
102 26 0.22
103 7 0.06
104 7 0.06
105 76 0.64
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
AAAAACAAAATTAATCTCACTTGAGATCATTTTCTCA
Found at i:43161 original size:36 final size:36
Alignment explanation
Indices: 43116--43234 Score: 118
Period size: 36 Copynumber: 3.4 Consensus size: 36
43106 ACAAAGTTGA
*
43116 TCTCACTTGAGATCATTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
43152 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
* * * * * *
43188 TCTCATTTGAGACTATATCT-T-AAAGCAAAGTTCG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
*
43222 TCTCGCTTGAGAC
1 TCTCACTTGAGAC
43235 GTCATTTTCT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 21 0.30
35 9 0.13
36 40 0.57
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:43518 original size:29 final size:28
Alignment explanation
Indices: 43485--43549 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
43475 CAGTTTCTCG
43485 TGAATAAAAATCTTGGAGTTTGTTCCTTT
1 TGAATAAAAATCTTGGAG-TTGTTCCTTT
* * *
43514 TGAATAAATATCTTTGAGTTGTTTCTTT
1 TGAATAAAAATCTTGGAGTTGTTCCTTT
43542 TGAA-AAAA
1 TGAATAAAA
43550 TCTGTGAGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 3 0.09
28 13 0.41
29 16 0.50
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (28 bp):
TGAATAAAAATCTTGGAGTTGTTCCTTT
Found at i:43544 original size:28 final size:27
Alignment explanation
Indices: 43485--43558 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 27
43475 CAGTTTCTCG
*
43485 TGAATAAAAATCTTGGAGTTTGTTCCTTT
1 TGAAT-AAAATCTTTGAG-TTGTTCCTTT
*
43514 TGAATAAATATCTTTGAGTTGTTTCTTT
1 TGAATAAA-ATCTTTGAGTTGTTCCTTT
*
43542 TGAA-AAAATCTGTGAGT
1 TGAATAAAATCTTTGAGT
43559 CTATTTATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 9 0.22
27 3 0.07
28 16 0.39
29 13 0.32
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.45
Consensus pattern (27 bp):
TGAATAAAATCTTTGAGTTGTTCCTTT
Found at i:43646 original size:29 final size:27
Alignment explanation
Indices: 43604--43671 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
43594 ACAGTTTCTC
43604 TTGAAAAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAAAATCTTGGAG-TTGTTCCTT
* * *
43632 TTGAATAAATATCTTTGAGTTGTTTCTT
1 TTGAA-AAAAATCTTGGAGTTGTTCCTT
43660 TT-AAAAAAATCT
1 TTGAAAAAAATCT
43672 GTGAGTCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
26 7 0.20
27 2 0.06
28 15 0.43
29 11 0.31
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.46
Consensus pattern (27 bp):
TTGAAAAAAATCTTGGAGTTGTTCCTT
Found at i:43780 original size:28 final size:26
Alignment explanation
Indices: 43716--43796 Score: 90
Period size: 28 Copynumber: 3.0 Consensus size: 26
43706 TCTTGAGACA
* *
43716 GTTTCTCTTGGAAAAAATCTTGGAGTTT
1 GTTTCT-TTTGAAAAAATCTTTGAG-TT
*
43744 GTTCCTTTTGAATAAATATCTTTGAGTT
1 GTTTCTTTTGAA-AAA-ATCTTTGAGTT
*
43772 GTTTCTTTTGAAAAAATCTGTGAGT
1 GTTTCTTTTGAAAAAATCTTTGAGT
43797 CTATTTATTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
26 9 0.20
27 8 0.17
28 21 0.46
29 8 0.17
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.46
Consensus pattern (26 bp):
GTTTCTTTTGAAAAAATCTTTGAGTT
Found at i:43872 original size:118 final size:119
Alignment explanation
Indices: 43443--43957 Score: 863
Period size: 119 Copynumber: 4.3 Consensus size: 119
43433 TATTTGAATC
* * * *
43443 TTTTAAAACGATTTTTTTTTATCTCTTAAAGACAGTTTCTCGTGAATAAAAATCTTGGAGTTTGT
1 TTTTAAAACGA--TTTTTGTGTCTCTT-GAGACAGTTTCTCTTGAA-AAAAATCTTGGAGTTTGT
43508 TCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAAATCTGTGAGTCTATTTA
62 TCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAAATCTGTGAGTCTATTTA
43566 TTTTAAAACGATTTTTGTGTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTGGAGTTTGTTCCT
1 TTTTAAAACGATTTTTGTGTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTGGAGTTTGTTCCT
*
43631 TTTGAATAAATATCTTTGAGTTGTTTCTTTTAAAAAAATCTGTGAGTCTATTTA
66 TTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAAATCTGTGAGTCTATTTA
*
43685 TTTTAAAACGATTTTTGTGTCTCTTGAGACAGTTTCTCTTGGAAAAAATCTTGGAGTTTGTTCCT
1 TTTTAAAACGATTTTTGTGTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTGGAGTTTGTTCCT
43750 TTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAAATCTGTGAGTCTATTTA
66 TTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAAATCTGTGAGTCTATTTA
43804 TTTTAAAACGA-TTTTGTGTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTGGAGTTTGTTCCT
1 TTTTAAAACGATTTTTGTGTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTGGAGTTTGTTCCT
*
43868 TTTGAATAAATATCTTTGAGTTGTTTCTTTTG-AAAAATCTTTGAGTCTATTTA
66 TTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAAATCTGTGAGTCTATTTA
* * * * *
43921 TTTTGAAACAAAGTTTTGTCTCTCTTGAGACAATTTC
1 TTTTAAAAC-GATTTTTGTGTCTCTTGAGACAGTTTC
43958 GTGAAAAATC
Statistics
Matches: 377, Mismatches: 13, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
117 28 0.07
118 85 0.23
119 225 0.60
120 16 0.04
121 12 0.03
123 11 0.03
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.46
Consensus pattern (119 bp):
TTTTAAAACGATTTTTGTGTCTCTTGAGACAGTTTCTCTTGAAAAAAATCTTGGAGTTTGTTCCT
TTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAAATCTGTGAGTCTATTTA
Found at i:43883 original size:29 final size:27
Alignment explanation
Indices: 43841--43905 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 27
43831 ACAGTTTCTC
*
43841 TTGAAAAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAATATCTTGGAG-TTGTTCCTT
* *
43869 TTGAATAAATATCTTTGAGTTGTTTCTT
1 TTGAA-AAATATCTTGGAGTTGTTCCTT
43897 TTGAAAAAT
1 TTGAAAAAT
43906 CTTTGAGTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 4 0.12
28 18 0.55
29 11 0.33
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (27 bp):
TTGAAAAATATCTTGGAGTTGTTCCTT
Found at i:43913 original size:25 final size:25
Alignment explanation
Indices: 43846--43928 Score: 85
Period size: 26 Copynumber: 3.1 Consensus size: 25
43836 TTCTCTTGAA
* *
43846 AAAAATCTTGGAGTTTGTTCCTTTTG
1 AAAAATCTTTGAG-TTGTTTCTTTTG
43872 AATAAATATCTTTGAGTTGTTTCTTTTG
1 -A-AAA-ATCTTTGAGTTGTTTCTTTTG
* *
43900 AAAAATCTTTGAGTCTATTTATTTTG
1 AAAAATCTTTGAGT-TGTTTCTTTTG
43926 AAA
1 AAA
43929 CAAAGTTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
25 10 0.20
26 15 0.31
27 2 0.04
28 14 0.29
29 8 0.16
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.48
Consensus pattern (25 bp):
AAAAATCTTTGAGTTGTTTCTTTTG
Found at i:43947 original size:237 final size:239
Alignment explanation
Indices: 43472--43957 Score: 861
Period size: 237 Copynumber: 2.0 Consensus size: 239
43462 TATCTCTTAA
43472 AGACAGTTTCTCGTGAATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTT
1 AGACAGTTTCTCGTGAATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTT
43537 TCTTTTGAAAAAATCTGTGAGTCTATTTATTTTAAAACGATTTTTGTGTCTCTTGAGACAGTTTC
66 TCTTTTGAAAAAATCTGTGAGTCTATTTATTTTAAAACGATTTTTGTGTCTCTTGAGACAGTTTC
43602 TCTTGAAAAAAATCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTAAAAA
131 TCTTGAAAAAAATCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTAAAAA
* * *
43667 AATCTGTGAGTCTATTTATTTTAAAACGATTTTTGTGTCTCTTG
196 AATCTGTGAGTCTATTTATTTTAAAACAAGTTTTGTCTCTCTTG
* *
43711 AGACAGTTTCTCTTGGA-AAAAATCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTT
1 AGACAGTTTCTCGTGAATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTT
43775 TCTTTTGAAAAAATCTGTGAGTCTATTTATTTTAAAACGA-TTTTGTGTCTCTTGAGACAGTTTC
66 TCTTTTGAAAAAATCTGTGAGTCTATTTATTTTAAAACGATTTTTGTGTCTCTTGAGACAGTTTC
*
43839 TCTTGAAAAAAATCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTT-GAAA
131 TCTTGAAAAAAATCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTAAAAA
* *
43903 AATCTTTGAGTCTATTTATTTTGAAACAAAGTTTTGTCTCTCTTG
196 AATCTGTGAGTCTATTTATTTTAAAAC-AAGTTTTGTCTCTCTTG
*
43948 AGACAATTTC
1 AGACAGTTTC
43958 GTGAAAAATC
Statistics
Matches: 237, Mismatches: 9, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
236 28 0.12
237 107 0.45
238 87 0.37
239 15 0.06
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (239 bp):
AGACAGTTTCTCGTGAATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTT
TCTTTTGAAAAAATCTGTGAGTCTATTTATTTTAAAACGATTTTTGTGTCTCTTGAGACAGTTTC
TCTTGAAAAAAATCTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTAAAAA
AATCTGTGAGTCTATTTATTTTAAAACAAGTTTTGTCTCTCTTG
Found at i:44002 original size:52 final size:54
Alignment explanation
Indices: 43924--44027 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 54
43914 CTATTTATTT
*
43924 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCG-T-GAAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTTAAAAAAATCTTTGAGTC
*
43976 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTTAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTTAAAAAAATCTTTGAG
44028 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 34 0.71
53 1 0.02
54 13 0.27
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (54 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTTAAAAAAATCTTTGAGTC
Found at i:44049 original size:30 final size:30
Alignment explanation
Indices: 44015--44279 Score: 161
Period size: 30 Copynumber: 8.1 Consensus size: 30
44005 ATTTTGTTAA
* *
44015 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
1 AAAAATCTTTAAGATTGTTTCTTTGGAAAC
*
44045 AAAAATCTTTAAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTAAGATTGTTTCTTTGGAAAC
* ** *
44075 AAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATCT-TTAAGATTGTTTCTTTGGAAAC
*
44112 AAAAATCTTTAAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTAAGATTGTTTCTTTGGAAAC
* ** *
44142 AAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATCT-TTAAGATTGTTTCTTTGGAAAC
* *
44179 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTAAGATTGTTTCTTTGGAAAC
* ** *
44209 AAAATTTTGTCTCTTTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATC-TTTAAGATTGTTTCTTTGGAAAC
* *
44246 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTAAGATTGTTTCTTTGGAAAC
44276 AAAA
1 AAAA
44280 TTTTGTCTCT
Statistics
Matches: 178, Mismatches: 36, Indels: 42
0.70 0.14 0.16
Matches are distributed among these distances:
30 96 0.54
31 8 0.04
36 8 0.04
37 66 0.37
ACGTcount: A:0.33, C:0.11, G:0.12, T:0.44
Consensus pattern (30 bp):
AAAAATCTTTAAGATTGTTTCTTTGGAAAC
Found at i:44107 original size:67 final size:67
Alignment explanation
Indices: 44032--44311 Score: 524
Period size: 67 Copynumber: 4.2 Consensus size: 67
44022 TTTGAGATTG
44032 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
44097 AA
66 AA
44099 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
44164 AA
66 AA
* *
44166 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTTTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
44231 AA
66 AA
* *
44233 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAC
1 TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
44298 AA
66 AA
44300 TTTCTTTTGAAA
1 TTTCTTTTGAAA
44312 AAATCTTTGA
Statistics
Matches: 209, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 209 1.00
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTAAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:44657 original size:64 final size:63
Alignment explanation
Indices: 44578--44702 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 63
44568 GATGAGATCC
* *
44578 ATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAA
* * **
44642 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
44703 TACCAACCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 19 0.35
64 36 0.65
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:44886 original size:15 final size:15
Alignment explanation
Indices: 44868--44917 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
44858 GTTTCACTTA
44868 AAACATTTTCTCTTG
1 AAACATTTTCTCTTG
44883 AAACATTTTCTCTTG
1 AAACATTTTCTCTTG
*
44898 AAACATTTTCTCTTA
1 AAACATTTTCTCTTG
44913 AAACA
1 AAACA
44918 AGATCATCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (15 bp):
AAACATTTTCTCTTG
Found at i:44902 original size:30 final size:30
Alignment explanation
Indices: 44859--44917 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
44849 TTTTGAGTCG
*
44859 TTTCACTTAAAACATTTTCTCTTGAAACAT
1 TTTCACTTAAAACATTTTCTCTTAAAACAT
* *
44889 TTTCTCTTGAAACATTTTCTCTTAAAACA
1 TTTCACTTAAAACATTTTCTCTTAAAACA
44918 AGATCATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.44
Consensus pattern (30 bp):
TTTCACTTAAAACATTTTCTCTTAAAACAT
Found at i:45387 original size:40 final size:41
Alignment explanation
Indices: 45331--45566 Score: 149
Period size: 40 Copynumber: 5.5 Consensus size: 41
45321 ATGGCCAACT
* * *
45331 GTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATC
1 GTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGACC
* * **
45372 -TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CC
1 GTCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGACC
*
45414 GTCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCA-ACC
1 GTCCTCATCACGTAGGAACCGTGTCAT--CC--CC---AGA---CCAGACC
* * *
45464 GTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATC
1 GTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGACC
* * **
45505 -TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCA-ACC
1 GTCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGACC
*
45547 GTACTCATCACGTAGGAACC
1 GTCCTCATCACGTAGGAACC
45567 ATGTTATCAC
Statistics
Matches: 150, Mismatches: 25, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
40 55 0.37
41 2 0.01
42 3 0.02
43 52 0.35
45 2 0.01
46 2 0.01
47 1 0.01
48 2 0.01
50 31 0.21
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (41 bp):
GTCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGACC
Found at i:45422 original size:43 final size:43
Alignment explanation
Indices: 45372--45566 Score: 164
Period size: 43 Copynumber: 4.4 Consensus size: 43
45362 AGACCAGATC
* *
45372 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCAACCATAGATAACCAACCG
* * **
45415 TCCTCATCACGTAGGAACCGTGTTATCACCTTCCTAAAGATGGCCAACCG
1 TCCTCATCACGTAGGAACCGTG---TCA---ACC-ATAGATAACCAACCG
* * * ** *
45465 TCCTCATCATGTAGGAATCGTGTCATCCCCAG---ACCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCAACCATAGATAACCA-ACCG
*
45505 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAACCG
1 TCCTCATCACGTAGGAACCGTGTCAACCATAGATAACCAACCG
*
45548 TACTCATCACGTAGGAACC
1 TCCTCATCACGTAGGAACC
45567 ATGTTATCAC
Statistics
Matches: 119, Mismatches: 21, Indels: 24
0.73 0.13 0.15
Matches are distributed among these distances:
40 29 0.24
41 2 0.02
42 2 0.02
43 44 0.37
44 3 0.03
46 3 0.03
47 3 0.03
49 2 0.02
50 31 0.26
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (43 bp):
TCCTCATCACGTAGGAACCGTGTCAACCATAGATAACCAACCG
Found at i:45557 original size:133 final size:133
Alignment explanation
Indices: 45319--45662 Score: 539
Period size: 133 Copynumber: 2.6 Consensus size: 133
45309 TAACTCCTTT
*
45319 AGATGGCCAACTGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
1 AGATGGCCAACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
* * *
45384 AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTCC
66 AGGAGCCGTGTCAACCATAGATAACCAACCGTACTCATCACGTAGGAACCATGTTATCACCTTCC
45449 TAA
131 TAA
45452 AGATGGCCAACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
1 AGATGGCCAACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
45517 AGGAGCCGTGTCAACCATAGATAACCAACCGTACTCATCACGTAGGAACCATGTTATCACCTTCC
66 AGGAGCCGTGTCAACCATAGATAACCAACCGTACTCATCACGTAGGAACCATGTTATCACCTTCC
45582 TAA
131 TAA
* * * * ** *
45585 AGATGGCCAGAAC-TCTTCATCACGTATGAGCCGTGTCATCCACC-GACCAAATCTCCTCATCAC
1 AGATGGCCA-ACCGTCCTCATCATGTAGGAATCGTGTCATCC-CCAGACCAGATCTCCTCATCAC
* *
45648 GTAGGAACTGTGTCA
64 GTAGGAGCCGTGTCA
45663 CCCTTAGACG
Statistics
Matches: 196, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
133 192 0.98
134 4 0.02
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.23
Consensus pattern (133 bp):
AGATGGCCAACCGTCCTCATCATGTAGGAATCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
AGGAGCCGTGTCAACCATAGATAACCAACCGTACTCATCACGTAGGAACCATGTTATCACCTTCC
TAA
Found at i:45704 original size:43 final size:39
Alignment explanation
Indices: 45594--45704 Score: 105
Period size: 40 Copynumber: 2.7 Consensus size: 39
45584 AAGATGGCCA
* * *
45594 GAACTCTTCATCACGTATGAGCCGTGTCATCCACCGACC
1 GAACTCTTCATCACGTATGAGCAGTGTCACCCAACGACC
* * * * *
45633 AAATCTCCTCATCACGTAGGAACTGTGTCACCCTTAGACGACCC
1 GAA-CTCTTCATCACGTATGAGCAGTGTCACCC--A-ACGA-CC
45677 GAACTCTTCATCACGTATGAGCAGTGTC
1 GAACTCTTCATCACGTATGAGCAGTGTC
45705 GTCCCCAACA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
39 2 0.04
40 24 0.44
42 1 0.02
43 24 0.44
44 4 0.07
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.24
Consensus pattern (39 bp):
GAACTCTTCATCACGTATGAGCAGTGTCACCCAACGACC
Found at i:45878 original size:3 final size:3
Alignment explanation
Indices: 45870--45924 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
45860 TCTAATTTTA
*
45870 ATT ATT ATT ATT ATT GTT ATT ATT ATT ATGT -TT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT -ATT ATT ATT
45916 ATT ATT ATT
1 ATT ATT ATT
45925 TTTGCAGGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 1 0.02
3 42 0.89
4 4 0.09
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:47737 original size:19 final size:19
Alignment explanation
Indices: 47696--47738 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
47686 ATTCCTTTTG
* **
47696 TATGTACTTATTTTTATGT
1 TATGTACTTATTTATATCA
*
47715 TATGTATTTATTTATATCA
1 TATGTACTTATTTATATCA
47734 TATGT
1 TATGT
47739 GAATTAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (19 bp):
TATGTACTTATTTATATCA
Found at i:50709 original size:59 final size:60
Alignment explanation
Indices: 50637--50782 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 60
50627 TTAAAAGGTT
*
50637 AAAGTATAC-AAATGGTCCCTCGACTATAGGATGTT-GTTTGTCAAGTTCC-TCGACTATCA
1 AAAGT-TACAAAATGGTCCCTCGACTATAGGATGTTACTTTGTCAAG-TCCATCGACTATCA
* * ** *
50696 AAAGTTACAAAATGATCCC-CCAGCTATAGGATGTTACTTTGTTGAGTCCATCGACTATTA
1 AAAGTTACAAAATGGTCCCTCGA-CTATAGGATGTTACTTTGTCAAGTCCATCGACTATCA
*
50756 AAAGTTACAAAATAGTCACCT-GACTAT
1 AAAGTTACAAAATGGTC-CCTCGACTAT
50783 TCATTATGTT
Statistics
Matches: 72, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
58 5 0.07
59 29 0.40
60 35 0.49
61 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCTCGACTATAGGATGTTACTTTGTCAAGTCCATCGACTATCA
Found at i:51453 original size:26 final size:26
Alignment explanation
Indices: 51419--51471 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
51409 TTATTATAGA
51419 AAAAATATGATTAAATAAGTTCCCAG
1 AAAAATATGATTAAATAAGTTCCCAG
*
51445 AAAAATATGATTAAATAAGTTCTCAG
1 AAAAATATGATTAAATAAGTTCCCAG
51471 A
1 A
51472 TTTAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.28
Consensus pattern (26 bp):
AAAAATATGATTAAATAAGTTCCCAG
Found at i:56358 original size:318 final size:318
Alignment explanation
Indices: 55781--56420 Score: 1253
Period size: 318 Copynumber: 2.0 Consensus size: 318
55771 TGTGGAGACC
55781 GATGGAGAAGTGAAATCTAAAACTGATTTGGTTAAGGATTCGAGAGAAGAGGATGAATCTTGTAT
1 GATGGAGAAGTGAAATCTAAAACTGATTTGGTTAAGGATTCGAGAGAAGAGGATGAATCTTGTAT
55846 TGAAATTGTGGATCAGGACAAGGAATCGATGGAATTGTGCCACGTGGACGCTCCTGTTGATGAAC
66 TGAAATTGTGGATCAGGACAAGGAATCGATGGAATTGTGCCACGTGGACGCTCCTGTTGATGAAC
*
55911 AAAATTCAGTGGATCTTGTTCGGAGTGGTCCTGTTTTTGCAATTAATGCTGAAAATGGTGTGCCA
131 AAAATTCAGTGGATCTTGCTCGGAGTGGTCCTGTTTTTGCAATTAATGCTGAAAATGGTGTGCCA
55976 GAAACTGCCACGACTGATCAGAATGAAGTCTCTGAATCAGCTGAAGATGTTTCTGATGCTAACAA
196 GAAACTGCCACGACTGATCAGAATGAAGTCTCTGAATCAGCTGAAGATGTTTCTGATGCTAACAA
56041 TATAGGTGAACACACTGGTTCAGAAGCTGCTGCTGTTGACTCCAGTGATAAACAGAGT
261 TATAGGTGAACACACTGGTTCAGAAGCTGCTGCTGTTGACTCCAGTGATAAACAGAGT
56099 GATGGAGAAGTGAAATCTAAAACTGATTTGGTTAAGGATTCGAGAGAAGAGGATGAATCTTGTAT
1 GATGGAGAAGTGAAATCTAAAACTGATTTGGTTAAGGATTCGAGAGAAGAGGATGAATCTTGTAT
*
56164 TGAAATTGTGGATCAGGACAAGGAATCGATGGAATTGTGCCACGTGGAGGCTCCTGTTGATGAAC
66 TGAAATTGTGGATCAGGACAAGGAATCGATGGAATTGTGCCACGTGGACGCTCCTGTTGATGAAC
56229 AAAATTCAGTGGATCTTGCTCGGAGTGGTCCTGTTTTTGCAATTAATGCTGAAAATGGTGTGCCA
131 AAAATTCAGTGGATCTTGCTCGGAGTGGTCCTGTTTTTGCAATTAATGCTGAAAATGGTGTGCCA
*
56294 GAAACTGCCACGGCTGATCAGAATGAAGTCTCTGAATCAGCTGAAGATGTTTCTGATGCTAACAA
196 GAAACTGCCACGACTGATCAGAATGAAGTCTCTGAATCAGCTGAAGATGTTTCTGATGCTAACAA
56359 TATAGGTGAACACACTGGTTCAGAAGCTGCTGCTGTTGACTCCAGTGATAAACAGAGT
261 TATAGGTGAACACACTGGTTCAGAAGCTGCTGCTGTTGACTCCAGTGATAAACAGAGT
56417 GATG
1 GATG
56421 AGATTTCTTC
Statistics
Matches: 319, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
318 319 1.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (318 bp):
GATGGAGAAGTGAAATCTAAAACTGATTTGGTTAAGGATTCGAGAGAAGAGGATGAATCTTGTAT
TGAAATTGTGGATCAGGACAAGGAATCGATGGAATTGTGCCACGTGGACGCTCCTGTTGATGAAC
AAAATTCAGTGGATCTTGCTCGGAGTGGTCCTGTTTTTGCAATTAATGCTGAAAATGGTGTGCCA
GAAACTGCCACGACTGATCAGAATGAAGTCTCTGAATCAGCTGAAGATGTTTCTGATGCTAACAA
TATAGGTGAACACACTGGTTCAGAAGCTGCTGCTGTTGACTCCAGTGATAAACAGAGT
Found at i:56704 original size:120 final size:119
Alignment explanation
Indices: 56470--57557 Score: 1104
Period size: 120 Copynumber: 9.1 Consensus size: 119
56460 CTAATGGTGT
* * * * ** *
56470 TGAAGCCAATGTTCTCGATTTCAGGTCTAAAGGGAATGAGGAATCTGAAATGGTTGTAGCTGATG
1 TGAA-CCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
* * * * * * *
56535 ATAGTGATTACAATGTAAATGGTCTAGCTAATGATAGTGCTAAAGCCCCTGCCTC
65 ATGGTGATTGCAATGGAAATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
* * * * * * *
56590 CGTAA-CATATGATGTTGATTCCAGGTCAAAAGAAAATGAGGGCTCTGAAACGGCTGTAGCTAAT
1 TG-AACCA-ATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGAT
* * * * * * *
56654 TATAGTGATTACAATGGAAATGATATAGCTAATGATAGTGCTAAGGCCCCTGCCTC
64 GATGGTGATTGCAATGGAAATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
* * * * * * * *
56710 CGTAGCATATGATGTTGATTCCAGGTCAAAAGAAAATGAGGGCTCTGAAATGGCTGTAGCTGATT
1 TGAACCA-ATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
* * * *
56775 CTGGTGATTGCAATGGAGAA-GGCTTAGCTAATGGTAGTGCTAAGGCCAGTGTCTC
65 ATGGTGATTGCAATGGA-AATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
* * * * * *
56830 TGAAGCCAATTTTCTCGATTTCAGATCAAAAGAGAATAAGGGCTCTGAAATGGCTGTAGCTGCTG
1 TGAA-CCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
* * * *
56895 ATGGTGATTGCAATGGAGATGGTTTAGCTAATGATGGTGCCAAGGCCACTGTGTC
65 ATGGTGATTGCAATGGAAATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
* * *
56950 TGAAGCCAATGTTCTCGATTCCAGGTCAACAGAGAATGAGGACTCTGAAATGGCTGTAGCTGATG
1 TGAA-CCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
*
57015 ATGGTGATTGCAGTGGAGAA-GGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
65 ATGGTGATTGCAATGGA-AATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
* * *
57070 TGAAGCCAATGTTATCGATTCCAAGTCAAAAGAGAACG-GAGGCTCTGAAATGGTTGTAGCTGAT
1 TGAA-CCAATGTTATCGATTCCAGGTCAAAAGAGAATGAG-GGCTCTGAAATGGCTGTAGCTGAT
* *
57134 GATGGTGATTGCAATGGAAATGCTTTAGCTAATGATAATG-TCAAGGCCACTGTCTC
64 GATGGTGATTGCAATGGAAATGGTTTAGCTAATGATAGTGCT-AAGGCCACTGTCTC
** * * * *
57190 TGTCGCCGATGTTATCGATACCAGGTTAAAAGAGAACG-GAGGCTCTGAAATGGCTGTAGCTGAT
1 TG-AACCAATGTTATCGATTCCAGGTCAAAAGAGAATGAG-GGCTCTGAAATGGCTGTAGCTGAT
* * *
57254 GATGGTGATTGCAATGG-AATTGTGTTAGCTAATGATAGTG-TCAAGTCCACTGTCTT
64 GATGGTGATTGCAATGGAAATGGT-TTAGCTAATGATAGTGCT-AAGGCCACTGTCTC
** *** * *
57310 TGAAGCCAATGTTATTTATTCCAGGTCAAAAGAGACCAAGGGCTCTGAAATAGTTGTAGCTGATG
1 TGAA-CCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATG
* ** * * *
57375 ATGGCGATCCCAATGGAGATGGTTTAGCTAGTGATAGTGCTAAGGCCACTGCCTC
65 ATGGTGATTGCAATGGAAATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
* **
57430 TG----AA-GTTCTCGATTCCAGGTTGAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATGA
1 TGAACCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATGA
** * * * * * *
57490 TGGCAACTGCAATGGAGATGATTTAGTTAATGTTAGTTCTAAGGCCACTGTCTC
66 TGGTGATTGCAATGGAAATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
57544 TGAAGCCAATGTTA
1 TGAA-CCAATGTTA
57558 GTGCTAAGGC
Statistics
Matches: 820, Mismatches: 126, Indels: 44
0.83 0.13 0.04
Matches are distributed among these distances:
114 92 0.11
115 2 0.00
119 14 0.02
120 699 0.85
121 13 0.02
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (119 bp):
TGAACCAATGTTATCGATTCCAGGTCAAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATGA
TGGTGATTGCAATGGAAATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTCTC
Found at i:57565 original size:33 final size:33
Alignment explanation
Indices: 57518--57621 Score: 199
Period size: 33 Copynumber: 3.2 Consensus size: 33
57508 TGATTTAGTT
*
57518 AATGTTAGTTCTAAGGCCACTGTCTCTGAAGCC
1 AATGTTAGTGCTAAGGCCACTGTCTCTGAAGCC
57551 AATGTTAGTGCTAAGGCCACTGTCTCTGAAGCC
1 AATGTTAGTGCTAAGGCCACTGTCTCTGAAGCC
57584 AATGTTAGTGCTAAGGCCACTGTCTCTGAAGCC
1 AATGTTAGTGCTAAGGCCACTGTCTCTGAAGCC
57617 AATGT
1 AATGT
57622 AATCGATTCC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 70 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (33 bp):
AATGTTAGTGCTAAGGCCACTGTCTCTGAAGCC
Found at i:57842 original size:300 final size:295
Alignment explanation
Indices: 57300--57849 Score: 692
Period size: 300 Copynumber: 1.8 Consensus size: 295
57290 AGTGTCAAGT
* * ** * * * **
57300 CCACTGTCTTTGAAGCCAATGTTATTTATTCCAGGTCAAAAGAGACCAAGGGCTCTGAAATAGTT
1 CCACTGTCTCTGAAGCCAATGTAATCGATTCCAAGCCAAAAGAGAACAAGGGCTCTGAAATAGCC
* *
57365 GTAGCTGATGATGGCGATCCCAATGGAGATGGTTTAGCTAGTGATAGTGCTAAGGCCACTGCCTC
66 GTAGCTGATGATGACGATCCCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGCCTC
** *
57430 TGAAGTTCTCGATTCCAGGTTGAAAGAGAATGAGGGCTCTGAAATGGCTGTAGCTGATGATGGCA
131 TGAAGTTCTCGATTCCAGGTCAAAAGAGAATGAGAGCTCTGAAATGGCTGTAGCTGATGAT----
* * *
57495 ACTGCAATGGAGATGATTTAGTTAATGTTAGTTCTAAGGCCACTGTCTCTGAAGCCAATGTTAGT
192 A-TGCAATGGAGATGATTTAGTTAATGATAGTGCTAAGACCACTGTCTCTGAAGCCAATGTTAGT
57560 GCTAAGGCCACTGTCTCTGAAGCCAATGTTAGTGCTAAGG
256 GCTAAGGCCACTGTCTCTGAAGCCAATGTTAGTGCTAAGG
* **
57600 CCACTGTCTCTGAAGCCAATGTAATCGATTCCAAGCCAGAAGAGAATGAGGGCTCTGAAATAGCC
1 CCACTGTCTCTGAAGCCAATGTAATCGATTCCAAGCCAAAAGAGAACAAGGGCTCTGAAATAGCC
* * **
57665 GTAGCTGATGATGACAGTTGCC-ATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGTTT
66 GTAGCTGATGATGAC-GATCCCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGCCT
* ** *
57729 CTGAAGCCAATGTTCTCGATTTCAGGTCAAAAGAGAATGAGATTTCTGAAATGGTTGTAGCTGAT
130 CT---G--AA-GTTCTCGATTCCAGGTCAAAAGAGAATGAGAGCTCTGAAATGGCTGTAGCTGAT
* *
57794 GAT-TGCGATGGAGATGGTTTAGCTT-ATGATAGTGCTAAGACCACTGTCTCTGAAGC
189 GATATGCAATGGAGATGATTTAG-TTAATGATAGTGCTAAGACCACTGTCTCTGAAGC
57850 TGCTGTAGAT
Statistics
Matches: 212, Mismatches: 30, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
300 153 0.72
301 6 0.03
303 1 0.00
305 2 0.01
306 50 0.24
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (295 bp):
CCACTGTCTCTGAAGCCAATGTAATCGATTCCAAGCCAAAAGAGAACAAGGGCTCTGAAATAGCC
GTAGCTGATGATGACGATCCCAATGGAGATGGTTTAGCTAATGATAGTGCTAAGGCCACTGCCTC
TGAAGTTCTCGATTCCAGGTCAAAAGAGAATGAGAGCTCTGAAATGGCTGTAGCTGATGATATGC
AATGGAGATGATTTAGTTAATGATAGTGCTAAGACCACTGTCTCTGAAGCCAATGTTAGTGCTAA
GGCCACTGTCTCTGAAGCCAATGTTAGTGCTAAGG
Found at i:61108 original size:21 final size:21
Alignment explanation
Indices: 61082--61131 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
61072 AACACGAGAG
*
61082 AAAACAGCTCCCGCAAAAGCT
1 AAAACAGCTCCCACAAAAGCT
*
61103 AAAACAGCTCCCACGAAAGCT
1 AAAACAGCTCCCACAAAAGCT
*
61124 GAAACAGC
1 AAAACAGC
61132 AAAGGATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.32, G:0.16, T:0.08
Consensus pattern (21 bp):
AAAACAGCTCCCACAAAAGCT
Found at i:64464 original size:97 final size:98
Alignment explanation
Indices: 64319--64506 Score: 245
Period size: 97 Copynumber: 1.9 Consensus size: 98
64309 CCACCGATGT
* * * *
64319 TTGAGTAAGTTTTTCTTTTCTCCATTGATATTTTAGAAGTAACGATTTAAACACTAATATTATCG
1 TTGAGTAAATTTATCTTTTCTCCATTGATATTTTAAAAGTAACGATTTAAACACTAATATTATCA
* *
64384 ATTTATAACAAATCGATCATTCACCGCTGATAC
66 ATTTACAACAAATCGACCATTCACCGCTGATAC
* * * * *
64417 TTGAGTAAATTTATCTTTT-TTCATTGATATTTTAAAATTAA-GTATTTAAATATTGATATTATC
1 TTGAGTAAATTTATCTTTTCTCCATTGATATTTTAAAAGTAACG-ATTTAAACACTAATATTATC
*
64480 AATTTACAATAAATCGACCATTCACCG
65 AATTTACAACAAATCGACCATTCACCG
64507 TTAATAATCA
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
96 1 0.01
97 59 0.77
98 17 0.22
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (98 bp):
TTGAGTAAATTTATCTTTTCTCCATTGATATTTTAAAAGTAACGATTTAAACACTAATATTATCA
ATTTACAACAAATCGACCATTCACCGCTGATAC
Found at i:76342 original size:16 final size:18
Alignment explanation
Indices: 76313--76349 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
76303 TATAATGTTT
*
76313 TAAATAATATAAATAT-A
1 TAAATAATAAAAATATCA
76330 TAAA-AATAAAAATATCA
1 TAAATAATAAAAATATCA
76347 TAA
1 TAA
76350 TAAGAATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAATAATAAAAATATCA
Done.